The invention claimed herein relates to the field of Josephson junction fabrication processes. Current existing processes for construction of Josephson junctions typically utilize an anodic anodization process to achieve device passivation/isolation. Unfortunately, anodization results in consumption of ˜60-80 nm of the superconductor film (e.g. Nb) and can cause degradation of the active tunneling barrier films and interfaces, therefore limiting the minimum device area, final achievable circuit density, and overall circuit reliability.